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Volume 69, Issue 11

sp. nov., isolated from sea water Free

Abstract

A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is (96.4 %), but the new isolate formed an independent phyletic line within the genus Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140 possessed C 2-OH, Cω7 and/or Cω6, and Cω7 and/or Cω6 as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140 should be classified as a novel species in the genus The type strain is LPB0140 (=KACC18891=JCM31568).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): sphingolipid , Sphingorhabdus and Sphingorhabdus lutea
© 2019 The Authors
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2019-11-01
2024-05-19
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References

  1. Jogler M, Chen H, Simon J, Rohde M, Busse H-J et al. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int J Syst Evol Microbiol 2013; 63:1342–1349 [View Article]
     [Google Scholar]
  2. Parte AC. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article]
     [Google Scholar]
  3. Yoon SH, Sm H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
     [Google Scholar]
  4. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article]
     [Google Scholar]
  5. Kumar S, Stecher G, Tamura K. MEga7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
     [Google Scholar]
  6. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012; 61:539–542 [View Article]
     [Google Scholar]
  7. Yang S-Z, Xiong X, Feng G-D, Li H-P, Zhu H-H. Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus . Int J Syst Evol Microbiol 2017; 67:4328–4331 [View Article]
     [Google Scholar]
  8. Subhash Y, Sasikala C, Ramana CV. Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish. Int J Syst Evol Microbiol 2014; 64:2238–2243 [View Article]
     [Google Scholar]
  9. Shin S-K, Kim E, Choi S, Yi H. Cochleicola gelatinilyticus gen. nov., sp. nov., Isolated from a marine gastropod, Reichia luteostoma . J Microbiol Biotechnol 2016; 26:1439–1445 [View Article]
     [Google Scholar]
  10. Gerhardt P. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  11. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  12. da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 2011; 38:197–206
     [Google Scholar]
  13. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  14. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
     [Google Scholar]
  15. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
     [Google Scholar]
  16. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  17. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article]
     [Google Scholar]
  18. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
     [Google Scholar]
  19. Chen H, Piao AL, Tan X, Nogi Y, Yeo J et al. Sphingorhabdus buctiana sp. nov., isolated from fresh water, and reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. Antonie van Leeuwenhoek 2018; 111:323–331 [View Article][PubMed]
     [Google Scholar]
  20. Park J-M, Park S, Jung Y-T, Kim H, Lee J-S et al. Sphingorhabdus arenilitoris sp. nov., isolated from a coastal sand, and reclassification of Sphingopyxis rigui as Sphingorhabdus rigui comb. nov. and Sphingopyxis wooponensis as Sphingorhabdus wooponensis comb. nov. Int J Syst Evol Microbiol 2014; 64:2551–2557 [View Article]
     [Google Scholar]
  21. Baik KS, Choe HN, Park SC, Hwang YM, Kim EM et al. Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis . Int J Syst Evol Microbiol 2013; 63:1297–1303 [View Article]
     [Google Scholar]
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Sphingorhabdus lutea sp. nov., isolated from sea water
Int J Syst Evol Microbiol 69, 3593 (2019); https://doi.org/10.1099/ijsem.0.003662
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